Mercurial > repos > ecology > data_paper_from_eml

annotate map_geographical_coverage.R @ 0:4a468c0c2260 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
author ecology
date Tue, 15 Oct 2024 20:33:32 +0000
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4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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1 #From https://github.com/TanguyGen/metaCure/blob/main/R/eml_down.R
4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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2 #Modified by Seguineau Pauline (2024-10-15)
4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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3 library(dplyr)
4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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4 library(xslt)
4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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5 library(xml2)
4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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6 library(mapview)
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7 library(leaflet)
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8
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9 args = commandArgs(trailingOnly=TRUE)
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10 if (length(args)==0)
4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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11 {
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12 stop("This tool needs at least one argument")
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13 }else{
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14 data <- args[1]
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15 }
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17 #' map_geographical_coverage
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18 #'Make a map from EML
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19 #' @param eml Metadata using EML standard in XML format
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20 #'
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21 #' @return A map
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22 #' @export
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24 map_geographical_coverage <- function(eml){
4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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25 name <- xml2::xml_find_all(eml, "//geographicCoverage/geographicDescription")
4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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26 name <- unlist(xml2::as_list(name))
4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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28 west <- xml2::xml_find_all(eml, "//geographicCoverage/boundingCoordinates/westBoundingCoordinate")
4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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29 west <- as.numeric(unlist(xml2::as_list(west)))
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31 east <- xml2::xml_find_all(eml, "//geographicCoverage/boundingCoordinates/eastBoundingCoordinate")
4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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32 east <- as.numeric(unlist(xml2::as_list(east)))
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34 north <- xml2::xml_find_all(eml, "//geographicCoverage/boundingCoordinates/northBoundingCoordinate")
4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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35 north <- as.numeric(unlist(xml2::as_list(north)))
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37 south <- xml2::xml_find_all(eml, "//geographicCoverage/boundingCoordinates/southBoundingCoordinate")
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38 south <- as.numeric(unlist(xml2::as_list(south)))
4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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40 geo_info <- data.frame(name = name, west = west, east = east, south = south, north = north)
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42 map <- leaflet(geo_info) %>%
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43 addProviderTiles("CartoDB.Positron")
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45 for (i in 1:nrow(geo_info)) {
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46 if (geo_info$west[i]==geo_info$east[i] && geo_info$south[i]==geo_info$north[i]){
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47 map <- map %>% addCircles(lng = geo_info$west[i] , lat= geo_info$south[i], fillColor = "transparent" ) %>% addScaleBar()}
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48
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49 else if(geo_info$west[i]!=geo_info$east[i] && geo_info$south[i]!=geo_info$north[i]){
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50 map <- map %>% addRectangles(lng1 = geo_info$west[i], lat1 = geo_info$south[i],
4a468c0c2260 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/make_data_paper_sketches commit 34f4e0604adc2a2ba4902ce6b8e6df2460eda292
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51 lng2 = geo_info$east[i], lat2 = geo_info$north[i], fillColor = "transparent") %>% addScaleBar()}
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52 }
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53 mapview::mapshot(map, file = "map.png",remove_controls = c("zoomControl", "layersControl", "homeButton","drawToolbar", "easyButton"))
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54 }
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56 doc <- read_xml(data)
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58 if (is.na(xml2::xml_find_first(doc, "//geographicCoverage"))){
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59 mes = "No geographic coverage found, skipping geographic coverage step."
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60 mes
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61 }else{
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62 map_geographical_coverage(doc)
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63 }
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